--- a/core_diversity_analyses.xml	Mon Jul 10 16:45:45 2017 -0400
+++ b/core_diversity_analyses.xml	Sat Aug 05 07:14:36 2017 -0400
@@ -1,46 +1,46 @@
-<tool id="qiime_core_diversity" name="Compute core set of diversity analyses" version="@WRAPPER_VERSION@.0">
-    <description>A workflow for running a core set of QIIME diversity analyses</description>
+<tool id="qiime_core_diversity" name="Run a core set of QIIME diversity analyses" version="@WRAPPER_VERSION@.0">
+    <description>(core_diversity_analyses)</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements"/>
     <version_command>core_diversity_analyses.py --version</version_command>
     <command detect_errors="aggressive"><![CDATA[
-        ## set matplotlib backend
-        echo "backend:agg" > matplotlibrc &&
+## set matplotlib backend
+echo "backend:agg" > matplotlibrc &&
 
-        core_diversity_analyses.py
-            --input_biom_fp '$input_biom_fp'
-            -o core_diversity_analyses
-            --mapping_fp '$mapping_fp'
-            --sampling_depth '$sampling_depth'
-            #if $parameter_fp
-                --parameter_fp '$parameter_fp'
-            #end if
-            $parallel
-            -O "\${GALAXY_SLOTS:-4}"
-            $phylogenetic.nonphylogenetic_diversity
-            #if str( $phylogenetic.nonphylogenetic_diversity ) == ""
-                --tree_fp '$phylogenetic.tree_fp'
-            #end if
-            $suppress_taxa_summary
-            $suppress_beta_diversity
-            $suppress_alpha_diversity
-            $suppress_group_significance
-            #if str( $categories ):
-                --categories '$categories'
-            #end if
+core_diversity_analyses.py
+    --input_biom_fp '$input_biom_fp'
+    -o core_diversity_analyses
+    --mapping_fp '$mapping_fp'
+    --sampling_depth '$sampling_depth'
+    #if $parameter_fp
+        --parameter_fp '$parameter_fp'
+    #end if
+    $parallel
+    -O "\${GALAXY_SLOTS:-4}"
+    $phylogenetic.nonphylogenetic_diversity
+    #if str( $phylogenetic.nonphylogenetic_diversity ) == ""
+        --tree_fp '$phylogenetic.tree_fp'
+    #end if
+    $suppress_taxa_summary
+    $suppress_beta_diversity
+    $suppress_alpha_diversity
+    $suppress_group_significance
+    #if str( $categories ):
+        --categories '$categories'
+    #end if
 
-        && mkdir -p '$html_report.files_path'
-        && cp -r core_diversity_analyses/* '$html_report.files_path'
-        && mv '$html_report.files_path/index.html' '$html_report'
+&& mkdir -p '$html_report.files_path'
+&& cp -r core_diversity_analyses/* '$html_report.files_path'
+&& mv '$html_report.files_path/index.html' '$html_report'
     ]]></command>
     <inputs>
         <param argument="--input_biom_fp" type="data" format="tabular,txt,biom,h5" label="OTU table"/>
         <param argument="--mapping_fp" type="data" format="tabular,txt,tsv" label="Mapping file" />
         <param argument="--sampling_depth" type="integer" value="" label="Sequencing depth to use for even sub-sampling and maximum rarefaction depth" help="To decide this value, review the output of the ‘biom summarize-table’"/>
         <param argument="--parameter_fp" type="data" format="txt" label="Parameter file" help="It specifies changes to the default behavior" optional="true"/>
-        <param argument="--parallel" type="boolean" label="Run in parallel where available?" truevalue="--parallel" falsevalue="" checked="true"/>
+        <param argument="--parallel" type="boolean" truevalue="--parallel" falsevalue="" checked="true" label="Run in parallel where available?"/>
         <conditional name="phylogenetic">
             <param argument="--nonphylogenetic_diversity" type="select" label="Apply non-phylogenetic alpha (chao1 and observed_otus) and beta (bray_curtis) diversity calculations?" help="This is useful if, for example, when working with non-amplicon BIOM tables, or if a reliable tree is not available">
                 <option value="--nonphylogenetic_diversity">Yes</option>
@@ -51,11 +51,11 @@
             </when>
             <when value="--nonphylogenetic_diversity"/>
         </conditional>
-        <param argument="--suppress_taxa_summary" type="boolean" label="Suppress generation of taxa summary plots?" truevalue="--suppress_taxa_summary" falsevalue="" checked="False"/>
-        <param argument="--suppress_beta_diversity" type="boolean" label="Suppress beta diversity analyses?" truevalue="--suppress_beta_diversity" falsevalue="" checked="False"/>
-        <param argument="--suppress_alpha_diversity" type="boolean" label="Suppress alpha diversity analyses?" truevalue="--suppress_alpha_diversity" falsevalue="" checked="False"/>
-        <param argument="--suppress_group_significance" type="boolean" label="Suppress OTU/category significance analysis?" truevalue="--suppress_group_significance" falsevalue="" checked="False"/>
-        <param argument="--categories" type="text" value="" label="Metadata category or categories to compare for categorical analyses (optional)" help="The column headers in the mapping file should be passed as a comma-separated list. By default, no categorical analyses are performed" optional="true"/>
+        <param argument="--suppress_taxa_summary" type="boolean" truevalue="--suppress_taxa_summary" falsevalue="" checked="false" label="Suppress generation of taxa summary plots?"/>
+        <param argument="--suppress_beta_diversity" type="boolean" truevalue="--suppress_beta_diversity" falsevalue="" checked="false" label="Suppress beta diversity analyses?"/>
+        <param argument="--suppress_alpha_diversity" type="boolean" truevalue="--suppress_alpha_diversity" falsevalue="" checked="false" label="Suppress alpha diversity analyses?"/>
+        <param argument="--suppress_group_significance" type="boolean" truevalue="--suppress_group_significance" falsevalue="" checked="false" label="Suppress OTU/category significance analysis?"/>
+        <param argument="--categories" type="text" value="" optional="true" label="Metadata category or categories to compare for categorical analyses (optional)" help="The column headers in the mapping file should be passed as a comma-separated list. By default, no categorical analyses are performed"/>
     </inputs>
     <outputs>
         <data name="html_report" format="html" label="${tool.name} on ${on_string}: Core diversity report"/>